How do you decrease the amount of bad bacteria in your tank?

My fish keeps getting sick and I don't know what I am doing wrong. He had tail/fin rot and lost a lot of his tail and a little of his fin. It went away. A few days ago it started again. Then, it appeared to stop. Now, I looked at him a few minutes ago and it looks like it is again starting. I don't see him biting his tail. Any suggestions? I have a 3 gallon carbon filtered tank. I change his water every week about 25%. He has two tall silk plants and two small ones that cover the gravel. Also, there is a heater in there and a thermometer. When I clean the tank I notice white flakes coming off of the heater suction cups and the thermometer suction cup. No idea what that is. My co-worker said it is salt because I use aquarium salt in the tank. I had the since the first week in June and there is only one betta in there. When I clean I can't absolutely get every piece of waste I see, but I try to get most of it. Little particles are hard to get at when I clean they come up and float around